Related papers: GMXPolymer: a generated polymerization algorithm b…
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and post-reaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that…
We introduce atomicrex, an open-source code for constructing interatomic potentials as well as more general types of atomic-scale models. Such effective models are required to simulate extended materials structures comprising many thousands…
In a recent paper, J. Chem. Phys. 162, 214101 (2025), a novel approach for the rigidification of a molecular cluster was proposed, in which starting with an all-atom (AA) potential, a coarse-grained (CG) potential for the associated cluster…
We introduce a new quantity to probe the glass transition. This quantity is a linear generalized compressibility which depends solely on the positions of the particles. We have performed a molecular dynamics simulation on a glass forming…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…
We propose a principled algorithm for robust Bayesian filtering and smoothing in nonlinear stochastic dynamic systems when both the transition function and the measurement function are described by non-parametric Gaussian process (GP)…
Dynamics of a charged particle in the canonical coordinates is a Hamiltonian system, and the well-known symplectic algorithm has been regarded as the de facto method for numerical integration of Hamiltonian systems due to its long-term…
In this work, methods are presented to automatically generate a fully atomistic LAMMPS models of arbitrary linear multiblock polyurethane copolymers. The routine detailed here receives as parameters the number of repeat units per hard…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
Understanding how polymer topology influences melt extrudability is critical for advancing material design in extrusion-based additive manufacturing. In this work, we develop a bottom-up, cross-scale modeling framework that integrates…
Polymer properties are inherently multi-scale in nature, where delicate local interaction details play a key role in describing their global conformational behavior. In this context, deriving coarse-grained (CG) multi-scale models for…
Stochastic multi-scale modeling and simulation for nonlinear thermo-mechanical problems of composite materials with complicated random microstructures remains a challenging issue. In this paper, we develop a novel statistical higher-order…
The conformational behavior of a coarse-grained finite polymer chain near an attractive spherical surface was investigated by means of multicanonical Monte Carlo computer simulations. In a detailed analysis of canonical equilibrium data…
For problems in astrophysics, planetary science and beyond, numerical simulations are often limited to simulating fewer particles than in the real system. To model collisions, the simulated particles (aka superparticles) need to be inflated…
Abstract polymer models are systems of weighted objects, called polymers, equipped with an incompatibility relation. An important quantity associated with such models is the partition function, which is the weighted sum over all sets of…
A computational method is presented which is capable to obtain low lying energy structures of topological amorphous systems. The method merges a differential mutation genetic algorithm with simulated annealing. This is done by incorporating…
We combine molecular dynamics simulations of deformations at the submicron scale with a continuum fracture mechanics calculation for the onset of crack propagation to predict the macroscopic fracture toughness of amorphous glassy polymers.…
We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning…
We study the effect of physical aging on the mechanical properties of a model polymer glass using molecular dynamics simulations. The creep compliance is determined simultaneously with the structural relaxation under a constant uniaxial…
Many glass-forming fluids exhibit a remarkable thermodynamic scaling in which dynamic properties, such as the viscosity, the relaxation time, and the diffusion constant, can be described under different thermodynamic conditions in terms of…